GEO DataSets

(Submitter supplied) Rationale: Changes in peripheral blood cell populations have been observed but not detailed at single-cell resolution in idiopathic pulmonary fibrosis (IPF). Objectives: To provide an atlas of the changes in the peripheral immune system in stable and progressive IPF. Methods: Peripheral blood mononuclear cells (PBMCs) from IPF patients and controls were profiled using 10x Chromium 5’ single-cell RNA sequencing (scRNA-seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

38 Samples

Download data: MTX, TSV

(Submitter supplied) Genome wide DNA methylation profiling of samples with/without chronic or acute Temporomandibular Disorders (TMD). The Illumina Infinium Human methylationEPIC Beadchip was used to obtain DNA methylation profiles across 1,051,943 CpGs in TMD samples. Samples included 452 non-TMD and 496 chronic TMD from OPPERA I, 36 healthy and 123 acute TMD from OPPERA II.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

1107 Samples

Download data: CSV, IDAT

(Submitter supplied) To determine gene expression changes that contribute to the development of COPD among smokers using high-throughput RNA sequencing in the peripheral blood of COPD patients. Total RNA sequencing was investigated by prospectively collecting lung function test results and whole blood samples from smokers who visited the outpatient department of respiratory medicine at three hospitals since 2020. This study confirmed gene expression differences in non-coding RNA in COPD patients according to the degree of airflow limitation through RNA-Seq transcriptome analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL30209

294 Samples

Download data: TXT

(Submitter supplied) Transcriptomic subtyping holds promise for personalized therapy in extensive stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers associated with long-term chemoimmunotherapy benefit in human ES-SCLC. Our work highlights that high intratumoral heterogeneity, lack of consistent association with outcome, and unclear subtype-specific target expression are major challenges for SCLC subtype-based precision oncology. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30173

175 Samples

Download data: DCC, PKC, PNG, XLSX

(Submitter supplied) Transcriptomic subtyping holds promise for personalized therapy in extensive stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers associated with long-term chemoimmunotherapy benefit in human ES-SCLC. Our work highlights that high intratumoral heterogeneity, lack of consistent association with outcome, and unclear subtype-specific target expression are major challenges for SCLC subtype-based precision oncology. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30173

121 Samples

Download data: DCC, PKC, PNG, XLSX

(Submitter supplied) Dysbiosis, or changes within the microbiome, is a common feature of solid tumors, however whether this dysbiosis directly contributes to tumor development is largely unknown. We previously characterized the human lung cancer microbiome and identified the Gram-negative Acidovorax temperans as enriched in tumors and associated with smoking status and TP53 mutations. To determine if A. temperans exposure could contribute to the development of lung cancer, we investigated its effect in a genetically engineered mouse model of lung adenocarcinoma driven by mutant Kras and Tp53. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

45 Samples

Download data: TXT

(Submitter supplied) Fibroblast growth factor (FGF) 10 is essential for lung morphogenesis and polymorphisms in the Fgf10 region are linked with higher susceptibility towards COPD in human patients. We found that FGF10 signaling is impaired in lung septal wall compartment from COPD patients. Mice with impaired FGF10 signaling (Fgf10+/-) were more prone to develop cigarette smoke (CS)-induced emphysema and pulmonary hypertension (PH). more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21810

68 Samples

Download data: GPR

(Submitter supplied) This study aims to determine how gene expression in the lung of mice is affected by cigarette smoking during infection with an H7N9 influenza virus.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

80 Samples

Download data: TXT

(Submitter supplied) DNA methylation analysis was performed for buccal samples from children exposed in utero to maternal smoking during pregnancy (with or without vitamin C supplementation) and in a smaller number of non-smoker controls

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

359 Samples

Download data: IDAT, TXT

(Submitter supplied) Precision medicine's potential to transform complex autoimmune-disease treatment is often challenged by limited data availability and inadequate sample size when compared to the number of molecular features found in high-throughput multi-omics datasets. Addressing this issue, the novel framework PRoBeNet (Predictive Response Biomarkers using Network medicine) was developed. ProBeNet operates under the hypothesis that the therapeutic effect of a drug propagates through a protein–protein interaction network to reverse disease states. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV

(Submitter supplied) Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, and is even more in women. EGFR mutations and ALK fusions are major alterations observed in NSLA. We have focused on NSLA without EGFR and ALK alteration (NENA) rather than NSLA with EGFR and ALK (EA). First, we selected 141 NSLA tissues, and performed proteogenomic analyses including the whole-genome sequencing (WGS), transcriptome, methylation EPIC array, total proteome and phosphoproteome. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

141 Samples

Download data: IDAT, TXT

(Submitter supplied) Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, and is even more in women. EGFR mutations and ALK fusions are major alterations observed in NSLA. We have focused on NSLA without EGFR and ALK alteration (NENA) rather than NSLA with EGFR and ALK (EA). First, we selected 141 NSLA tissues, and performed proteogenomic analyses including the whole-genome sequencing (WGS), transcriptome, methylation EPIC array, total proteome and phosphoproteome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

141 Samples

Download data: TAB

(Submitter supplied) RNAseq analysis of placental gene expression in samples obtained from 59 smokers (enrolled in the VCSIP RCT: NCT03203603) and 20 never-smokers for reference.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

79 Samples

Download data: CSV

(Submitter supplied) Background. The unknown tissue of origin in head and neck cancer of unknown primary (hnCUP) leads to invasive diagnostic procedures and unspecific and potentially inefficient treatment options for patients. The most common histological subtype, squamous cell carcinoma, can stem from various tumor primary sites, including the oral cavity, oropharynx, larynx, head and neck skin, lungs, and esophagus. DNA methylation profiles are highly tissue-specific and have been successfully used to classify tissue origin. We therefore developed a support vector machine (SVM) classifier trained with publicly available DNA methylation profiles of commonly cervically metastasizing squamous cell carcinomas (n = 1,103) in order to identify the primary tissue of origin of our own cohort of squamous cell hnCUP patient’s samples (n = 28). Methylation analysis was performed with Infinium MethylationEPIC v1.0 BeadChip by Illumina. Results. The SVM algorithm achieved the highest overall accuracy of tested classifiers, with 87%. Squamous cell hnCUP samples on DNA methylation level resembled squamous cell carcinomas commonly metastasizing into cervical lymph nodes. The most frequently predicted cancer localization was the oral cavity in 11 cases (39%), followed by the oropharynx and larynx (both 7, 25%), skin (2, 7%), and esophagus (1, 4%). These frequencies concord with the expected distribution of lymph node metastases in epidemiological studies. Conclusions. On DNA methylation level, hnCUP is comparable to primary tumor tissue cancer types that commonly metastasize to cervical lymph nodes. Our SVM-based classifier can accurately predict these cancers’ tissues of origin and could significantly reduce the invasiveness of hnCUP diagnostics and enable a more precise therapy after clinical validation.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

28 Samples

Download data: IDAT

(Submitter supplied) The autoantibodies in serum (IgG antibody labeled with Cy3 and IgM antibody labeled with Cy5) were quantified by serum incubation human protein microarray, and the data of normal people and lung cancer patients were compared to find the predictive markers of autoantibodies in lung cancer

Organism:

Homo sapiens

Type:

Protein profiling by protein array

Platforms:

GPL29809 GPL29810

196 Samples

Download data: GPR

(Submitter supplied) Objectives: Systemic inflammatory response syndrome (SIRS) is a frequent complication of cardiopulmonary bypass (CPB). SIRS is associated with significant morbidity and mortality, but its pathogenesis remains incompletely understood, and as a result biomarkers are lacking, and treatment remains expectant and supportive. This study aimed to understand the pathophysiological mechanisms driving SIRS induced by CPB and identify novel therapeutic targets that might reduce systemic inflammation and improve patient outcomes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

77 Samples

Download data: CSV

(Submitter supplied) Metastases in the brain are the most severe and devastating complication of cancer. The incidence of brain metastasis is increasing. Therefore, the need of finding specific druggable targets for brain metastasis is demanding. The aim of this study was to compare the brain (immune) response to brain metastases of the most common tumor lineages, viz., lung adenocarcinoma and breast cancer. Targeted gene expression profiles of 11 brain metastasis of lung adenocarcinoma (BM-LUAD) were compared to 11 brain metastasis of breast cancer (BCBM) using NanoString nCounter PanCancer IO 360™ Panel. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL32069

22 Samples

Download data: CSV

(Submitter supplied) This study performed genomic sequencing on a rare phenotype of HPV-positive oropharyngeal squamous cell carcinoma which was resistant to standard of care platinum based chemoradiation treatment. Tissue was collected from archival FFPE when available from pretreatment and post treamtent samples from four patients and these were batch corrected to be compared to known HPV-positive tumors without recurrent disease

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

83 Samples

Download data: TXT

(Submitter supplied) Lung adenocarcinoma (LUAD) is one of the most common pathological and histological subtypes of primary lung cancer, with high morbidity and mortality. MicroRNAs (miRNAs) are endogenous small non-coding RNAs that regulate the expression of genes at post-transcriptional level. It was reported that A-to-I miRNA editing was decreased in tumors, suggesting the potential value of miRNA editing in cancer classification. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23227

38 Samples

Download data: XLSX

(Submitter supplied) We analyzed the transcriptome profiles of CD19+ B cells and CD4+ T cells from the peripheral blood of patients with multiple sclerosis (MS) immediately before and after relapse therapy with high-dose methylprednisolone (MP). High-density Clariom D Arrays for human were used to quantify the transcript levels. This GEO entry provides the processed data from the gene-level and exon-level workflows.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

48 Samples

Download data: CEL, CHP, TXT